merge files for aligning

[priya]

Hi,
I have 4 runs (4 fastq) raw data files for one sample. I would like to align the data, but wondering
1)can I concatate the 4 files into one file and then use the single file as Input to aligner tool(STAR, or Bowtie) or
2) Should I run aligment seperately on 4 fastq files and then use samtools to merge 4 bam files into single file.

which is the correct procedure to do..please guide me..
Thank you!

[dpryan]

If they came from the same library preparation then it doesn't matter which way you go about things. If they came from different library preps, you might get ever so slightly better results by treating them separately, due mostly to possible differences in insert sizes.

[swbarnes2]

It all amounts to the same thing in the end.